mythos.observables.diameter

Diameter observable.

Attributes

TARGETS

ERR_DISPLACEMENT_FN_REQUIRED

single_diameter_mapped

Classes

Diameter

Computes the helical diameter for each state.

Functions

single_diameter(→ mythos.utils.types.ARR_OR_SCALAR)

Computes the helical diameter of a base pair.

Module Contents

mythos.observables.diameter.TARGETS
mythos.observables.diameter.ERR_DISPLACEMENT_FN_REQUIRED = 'A displacement function is required for computing the helical diameter.'
mythos.observables.diameter.single_diameter(bp: jax.numpy.ndarray, back_sites: jax.numpy.ndarray, displacement_fn: collections.abc.Callable, sigma_backbone: float) → mythos.utils.types.ARR_OR_SCALAR[source]

Computes the helical diameter of a base pair.

Parameters:

  • bp (jnp.ndarray) – a 2-dimensional array containing the indices of the h-bonded nucleotides

  • back_sites (jnp.ndarray) – a 2-dimensional array containing the positions of the backbone sites

  • displacement_fn (Callable) – a function for computing displacements between two positions

  • sigma_backbone (float) – the excluded volume distance between backbone sites

Returns:

the helical diameter in Angstroms for each base pair

Return type:

jd_types.ARR_OR_SCALAR

mythos.observables.diameter.single_diameter_mapped
class mythos.observables.diameter.Diameter[source]

Bases: mythos.observables.base.BaseObservable

Computes the helical diameter for each state.

The helical diameter for a given base pair is defined as the furthest extent of the excluded volume. The diameter per state is the average over all (specified) base pairs.

Args: - bp: a 2-dimensional array containing the indices of the h-bonded nucleotides - displacement_fn: a function for computing displacements between two positions

h_bonded_base_pairs: jax.numpy.ndarray
displacement_fn: collections.abc.Callable
__post_init__() → None[source]

Validate the input.

__call__(trajectory: mythos.simulators.io.SimulatorTrajectory, sigma_backbone: float) → mythos.utils.types.ARR_OR_SCALAR[source]

Calculate the average helical diameter in Angstroms.

Parameters:

  • trajectory (jd_traj.Trajectory) – the trajectory to calculate the helical diameter for

  • sigma_backbone (float) – the excluded volume distance between backbone sites

Returns:

the average helical diameter in Angstroms for each state, so expect a size of (n_states,)

Return type:

jd_types.ARR_OR_SCALAR